Proteomic Profiling of Cerebrospinal Fluid

Cerebrospinal fluid (CSF) is a body fluid which has direct contact with the central nervous system, and as such, changes in its composition might be informative about various aspects of the brain. It has been postulated for quite a long time that proteomic analysis of CSF will reveal protein markers related to neurological disorders, their prognosis and early detection, efficacy of treatment, etc. Several proteomic profiling platforms provide tools to determine changes occurring in protein profiles of CSF reflecting physiological and pathological changes. Two major strategies are used. The first strategy is based on determining quantitative changes at the level of intact proteins followed by protein identification by tandem mass spectrometry of in-gel-digested protein spots. Usually, two-dimensional gel electrophoresis with DIGE technology is used. The second strategy is based on tryptic digestion of entire sample, labeling resulting peptides with mass tags and determining quantitative changes in protein content based on relative ratios of peptides. Typically iTRAQ^� technology is used. Regardless of the strategy used, samples of CSF need to be simplified by removing most abundant proteins constituting more than 90% of a total pool of proteins. Detailed protocols are presented in this chapter.